Dstara/api improvements

.github/workflows/github_actions.yml

@@ -1,13 +1,46 @@
 name: TileDB-Cloud-Java
 
 on:
+  workflow_dispatch:
   push:
     tags:
       - '*'
+    branches:
+      - master
+      - test-*
+  pull_request:
 
 jobs:
+  Examples:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout
+        uses: actions/checkout@v3
+
+      - run: |
+          unset SYSTEM
+          ./gradlew assemble;
+        shell: bash
+        name: assemble
+
+      - name: Run examples
+        env:
+          API_TOKEN: ${{ secrets.API_TOKEN }}
+        run: |
+          cd build/libs
+          rm *javadoc* *sources* *default*
+          p=$(readlink -f *.jar)
+          cd ../../src/main/java/examples
+          javac -cp $p *.java
+          for x in $(ls -1 *.java | sed 's/.java//'); 
+          do 
+          echo $x;
+          class_name=examples.$x; 
+          java -cp $p $class_name; 
+          done
   Release:
     if: startsWith(github.ref, 'refs/tags/')
+    needs: [Examples]
     name: Create-Release
     runs-on: ubuntu-latest
     steps:

build.gradle

@@ -27,7 +27,7 @@ apply plugin: 'java'
 apply plugin: 'com.diffplug.spotless'
 
 group 'io.tiledb'
-version = '0.1.1-SNAPSHOT'
+version = '0.2.1-SNAPSHOT'
 
 repositories {
     mavenCentral()
@@ -158,12 +158,10 @@ dependencies {
     implementation group: 'org.apache.arrow', name: 'arrow-vector', version: '9.0.0'
     implementation group: 'org.apache.arrow', name: 'arrow-compression', version: '9.0.0'
     implementation group: 'org.apache.arrow', name: 'arrow-memory-unsafe', version: '9.0.0'
-    implementation 'io.tiledb:tiledb-java:0.17.2'
     testImplementation 'org.junit.jupiter:junit-jupiter-api:5.8.2'
     testImplementation 'org.mockito:mockito-core:3.12.4'
     testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.8.2'
     testImplementation 'junit:junit:4.13.1'
-
 }
 
 import org.gradle.plugins.signing.Sign

src/main/java/examples/Examples.java

@@ -1,21 +1,22 @@
 package examples;
 
 // Import classes:
-import io.tiledb.cloud.TileDBClient;
-import io.tiledb.cloud.TileDBUDF;
-import io.tiledb.cloud.rest_api.ApiClient;
+import io.tiledb.cloud.*;
 import io.tiledb.cloud.rest_api.ApiException;
-import io.tiledb.cloud.TileDBLogin;
 import io.tiledb.cloud.rest_api.api.GroupsApi;
 import io.tiledb.cloud.rest_api.api.ArrayApi;
 import io.tiledb.cloud.rest_api.model.*;
+import jdk.swing.interop.SwingInterOpUtils;
+import org.apache.arrow.vector.ValueVector;
 
 import java.math.BigDecimal;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 
+import static io.tiledb.cloud.TileDBUtils.serializeArgs;
+
 public class Examples
 {
     public static void main(String[] args) {
@@ -24,7 +25,7 @@ public static void main(String[] args) {
         TileDBClient tileDBClient = new TileDBClient(
                 new TileDBLogin(null,
                         null,
-                        "<TILEDB_API_TOKEN>",
+                        System.getenv("API_TOKEN"),
                         true,
                         true,
                         true));
@@ -33,19 +34,35 @@ public static void main(String[] args) {
 //      to pass any credentials from now on. Just create the client as follows:
 //      TileDBClient tileDBClient = new TileDBClient();
 
-        ArrayApi apiInstance = new ArrayApi(tileDBClient.getApiClient());
 
 //        Uncomment to run whichever example you want
-//        runGenericUDF(tileDBClient);
-//        runArrayUDF(tileDBClient);
-//        runMultiArrayUDF(tileDBClient);
-//        getArraySchema(apiInstance);
-//        createArray(apiInstance);
-//        registerArray(apiInstance);
-//        listArrays(apiInstance);
-//        listGroups(defaultClient);
-//        deleteArray(apiInstance);
-//        deregisterArray(apiInstance);
+        runGenericUDF(tileDBClient);
+        runArrayUDF(tileDBClient);
+        runMultiArrayUDF(tileDBClient);
+        getArraySchema(tileDBClient);
+//        createArray(tileDBClient);
+//        registerArray(tileDBClient);
+        listArrays(tileDBClient);
+        listGroups(tileDBClient);
+//        deleteArray(tileDBClient);
+//        deregisterArray(tileDBClient);
+        runSQL(tileDBClient);
+        runSQLArrow(tileDBClient);
+
+    }
+
+    private static void runSQL(TileDBClient tileDBClient) {
+        SQLParameters sqlParameters = new SQLParameters();
+        sqlParameters.setQuery("SELECT * FROM `tiledb://TileDB-Inc/quickstart_sparse`");
+        TileDBSQL tileDBSQL = new TileDBSQL(tileDBClient, "TileDB-Inc", sqlParameters);
+        System.out.println(tileDBSQL.exec());
+    }
+
+    private static void runSQLArrow(TileDBClient tileDBClient) {
+        SQLParameters sqlParameters = new SQLParameters();
+        sqlParameters.setQuery("SELECT * FROM `tiledb://TileDB-Inc/quickstart_sparse`");
+        TileDBSQL tileDBSQL = new TileDBSQL(tileDBClient, "TileDB-Inc", sqlParameters);
+        Pair<ArrayList<ValueVector>, Integer> a = tileDBSQL.execArrow();
     }
 
     /**
@@ -59,11 +76,12 @@ private static void runGenericUDF(TileDBClient tileDBClient){
         HashMap<String,Object> arguments = new HashMap<>();
         arguments.put("arg1", "a1");
         arguments.put("arg2", "a2");
-        System.out.println(tileDBUDF.executeGeneric(genericUDF, arguments)); //could be JSON or Arrow
+        genericUDF.setArgument(serializeArgs(arguments));
+        System.out.println(tileDBUDF.executeGeneric(genericUDF)); //could be JSON or Arrow
     }
 
     /**
-     * Runs an array UDF on a TileDB Arrray
+     * Runs an array UDF on a TileDB Array
      * @param tileDBClient
      */
     public static void runArrayUDF(TileDBClient tileDBClient){
@@ -80,15 +98,18 @@ public static void runArrayUDF(TileDBClient tileDBClient){
         queryRanges.addRangesItem(range1);
         queryRanges.addRangesItem(range2);
 
-
         HashMap<String,Object> argumentsForArrayUDF = new HashMap<>();
         argumentsForArrayUDF.put("attr", "rows");
         argumentsForArrayUDF.put("scale", 9);
 
-        MultiArrayUDF multiArrayUDF = new MultiArrayUDF();
-        multiArrayUDF.setUdfInfoName("TileDB-Inc/array-udf");
-        multiArrayUDF.setRanges(queryRanges);
-        System.out.println(tileDBUDF.executeSingleArray(multiArrayUDF, argumentsForArrayUDF, "tiledb://TileDB-Inc/quickstart_sparse", "TileDB-Inc"));
+        GenericUDF genericUDF = new GenericUDF();
+        genericUDF.setUdfInfoName("TileDB-Inc/array-udf");
+        genericUDF.setArgument(serializeArgs(argumentsForArrayUDF));
+
+        UDFArrayDetails array = new UDFArrayDetails();
+        array.setUri("tiledb://TileDB-Inc/quickstart_sparse");
+
+        System.out.println(tileDBUDF.executeSingleArray(genericUDF, array, queryRanges, "TileDB-Inc"));
     }
 
     /**
@@ -117,7 +138,7 @@ public static void runMultiArrayUDF(TileDBClient tileDBClient){
 
         //array1
         UDFArrayDetails array1 = new UDFArrayDetails();
-        array1.setUri("tiledb://TileDB-Inc/dense-array");
+        array1.setUri("tiledb://shaunreed/dense-array");
         array1.setRanges(queryRanges);
         array1.setBuffers(Arrays.asList("rows", "cols", "a1"));
         arrays.add(array1);
@@ -135,17 +156,19 @@ public static void runMultiArrayUDF(TileDBClient tileDBClient){
         arguments.put("attr1", "a1");
         arguments.put("attr2", "a");
 
-        System.out.println(tileDBUDF.executeMultiArray(multiArrayUDF, arguments));
+        multiArrayUDF.setArgument(serializeArgs(arguments));
+
+        System.out.println(tileDBUDF.executeMultiArray(multiArrayUDF));
     }
 
     /**
      * Deregister an array
-     * @param apiInstance
      */
-    private static void deregisterArray(ArrayApi apiInstance)
+    private static void deregisterArray(TileDBClient tileDBClient)
     {
         String namespace = "<TILEDB_NAMESPACE>"; // String | namespace array is in (an organization name or user's username)
         String array = "<ARRAY_NAME>"; // String | name/uri of array that is url-encoded
+        ArrayApi apiInstance = new ArrayApi(tileDBClient.getApiClient());
         try {
             apiInstance.deregisterArray(namespace, array);
         } catch (ApiException e) {
@@ -159,13 +182,13 @@ private static void deregisterArray(ArrayApi apiInstance)
 
     /**
      * Delete an array
-     * @param apiInstance
      */
-    private static void deleteArray(ArrayApi apiInstance)
+    private static void deleteArray(TileDBClient tileDBClient)
     {
         String namespace = "<TILEDB_NAMESPACE>"; // String | namespace array is in (an organization name or user's username)
         String array = "<ARRAY_NAME>"; // String | name/uri of array that is url-encoded
         String contentType = "application/json"; // String | Content Type of input and return mime
+        ArrayApi apiInstance = new ArrayApi(tileDBClient.getApiClient());
         try {
             apiInstance.deleteArray(namespace, array, contentType);
         } catch (ApiException e) {
@@ -177,17 +200,13 @@ private static void deleteArray(ArrayApi apiInstance)
         }
     }
 
-    /**
-     * List groups
-     * @param defaultClient
-     */
-    private static void listGroups(ApiClient defaultClient)
+    private static void listGroups(TileDBClient tileDBClient)
     {
-        GroupsApi apiInstance = new GroupsApi(defaultClient);
+        GroupsApi apiInstance = new GroupsApi(tileDBClient.getApiClient());
         Integer page = null; // Integer | pagination offset
         Integer perPage = null; // Integer | pagination limit
         String search = null; // String | search string that will look at name, namespace or description fields
-        String namespace = "<TILEDB_NAMESPACE>"; // String | namespace
+        String namespace = "TileDB-Inc"; // String | namespace
         String orderby = null; // String | sort by which field valid values include last_accessed, size, name
         String permissions = null; // String | permissions valid values include read, read_write, write, admin
         List<String> tag = null; // List<String> | tag to search for, more than one can be included
@@ -208,13 +227,11 @@ private static void listGroups(ApiClient defaultClient)
 
     }
 
-    /**
-     * List arrays
-     * @param apiInstance
-     */
-    private static void listArrays(ArrayApi apiInstance)
+    private static void listArrays(TileDBClient tileDBClient)
     {
-        String namespace = "<TILEDB_NAMESPACE>"; // String | namespace array is in (an organization name or user's username)
+        String namespace = "dstara"; // String | namespace array is in (an organization name or user's username)
+        ArrayApi apiInstance = new ArrayApi(tileDBClient.getApiClient());
+
         try {
             List<ArrayInfo> result = apiInstance.getArraysInNamespace(namespace);
             System.out.println(result);
@@ -228,12 +245,14 @@ private static void listArrays(ArrayApi apiInstance)
     }
 
 
-    private static void getArraySchema(ArrayApi arrayApi){
-        String namespace = "<TILEDB_NAMESPACE>"; // String | namespace array is in (an organization name or user's username)
-        String array = "<ARRAY_URI>"; // String | name/uri of array that is url-encoded
+    private static void getArraySchema(TileDBClient tileDBClient){
+        String namespace = "TileDB-Inc"; // String | namespace array is in (an organization name or user's username)
+        String array = "quickstart_sparse"; // String | name/uri of array that is url-encoded
         String contentType = "application/json"; // String | Content Type of input and return mime
+        ArrayApi apiInstance = new ArrayApi(tileDBClient.getApiClient());
+
         try {
-            ArraySchema result = arrayApi.getArray(namespace, array, contentType);
+            ArraySchema result = apiInstance.getArray(namespace, array, contentType);
             System.out.println(result);
         } catch (ApiException e) {
             System.err.println("Exception when calling ArrayApi#getArray");
@@ -244,7 +263,7 @@ private static void getArraySchema(ArrayApi arrayApi){
         }
     }
 
-    private static void createArray(ArrayApi arrayApi){
+    private static void createArray(TileDBClient tileDBClient){
         String namespace = "<TILEDB_NAMESPACE>"; // String | namespace array is in (an organization name or user's username)
         String arrayName = "s3://<BUCKET-NAME>/my_array"; // String | name/uri of array that is url-encoded //
         String contentType = "application/json"; // String | Content Type of input and return mime
@@ -294,8 +313,10 @@ private static void createArray(ArrayApi arrayApi){
         schema.setCellOrder(Layout.ROW_MAJOR);
         System.out.println(schema);
 
+        ArrayApi apiInstance = new ArrayApi(tileDBClient.getApiClient());
+
         try {
-            arrayApi.createArray(namespace, arrayName, contentType, schema, null);
+            apiInstance.createArray(namespace, arrayName, contentType, schema, null);
         } catch (ApiException e) {
             System.err.println("Exception when calling ArrayApi#createArray");
             System.err.println("Status code: " + e.getCode());
@@ -305,14 +326,16 @@ private static void createArray(ArrayApi arrayApi){
         }
     }
 
-    public static void registerArray(ArrayApi arrayApi){
+    public static void registerArray(TileDBClient tileDBClient){
         String namespace = "<TILEDB_NAMESPACE>"; // String | namespace array is in (an organization name or user's username)
         String array = "s3://<BUCKET-NAME>/<ARRAY-URI>/"; // String | name/uri of array that is url-encoded
         ArrayInfoUpdate arrayMetadata = new ArrayInfoUpdate(); // ArrayInfoUpdate | metadata associated with array
         arrayMetadata.setUri("s3://<BUCKET-NAME>/<ARRAY-URI>/");
         arrayMetadata.setName("<ARRAY-NAME>");
+        ArrayApi apiInstance = new ArrayApi(tileDBClient.getApiClient());
+
         try {
-            ArrayInfo result = arrayApi.registerArray(namespace, array, arrayMetadata);
+            ArrayInfo result = apiInstance.registerArray(namespace, array, arrayMetadata);
             System.out.println(result);
         } catch (ApiException e) {
             System.err.println("Exception when calling ArrayApi#registerArray");

src/main/java/io/tiledb/cloud/Pair.java

@@ -0,0 +1,39 @@
+package io.tiledb.cloud;
+
+public class Pair<F, S> implements java.io.Serializable {
+    private F first;
+    private S second;
+
+    private Pair() {}
+
+    public Pair(F first, S second) {
+        this.first = first;
+        this.second = second;
+    }
+
+    public F getFirst() {
+        return first;
+    }
+
+    public void setFirst(F first) {
+        this.first = first;
+    }
+
+    public S getSecond() {
+        return second;
+    }
+
+    public void setSecond(S second) {
+        this.second = second;
+    }
+
+    /**
+     * Returns an empty Pair
+     *
+     * @return The Pair
+     */
+    public static Pair empty() {
+        return new Pair();
+    }
+}
+

src/main/java/io/tiledb/cloud/TileDBLogin.java

@@ -1,7 +1,5 @@
 package io.tiledb.cloud;
 
-import java.util.Objects;
-
 public class TileDBLogin {
     /** The client password */
     private String password;